MetaGaAP: A Novel Pipeline to Estimate Community Composition and Abundance from Non-Model Sequence DataReport as inadecuate


MetaGaAP: A Novel Pipeline to Estimate Community Composition and Abundance from Non-Model Sequence Data


MetaGaAP: A Novel Pipeline to Estimate Community Composition and Abundance from Non-Model Sequence Data - Download this document for free, or read online. Document in PDF available to download.

School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane City QLD 4000, Australia





*

Author to whom correspondence should be addressed.



Academic Editor: Jukka Finne

Abstract Next generation sequencing and bioinformatic approaches are increasingly used to quantify microorganisms within populations by analysis of ‘meta-barcode’ data. This approach relies on comparison of amplicon sequences of ‘barcode’ regions from a population with public-domain databases of reference sequences. However, for many organisms relevant ‘barcode’ regions may not have been identified and large databases of reference sequences may not be available. A workflow and software pipeline, ‘MetaGaAP,’ was developed to identify and quantify genotypes through four steps: shotgun sequencing and identification of polymorphisms in a metapopulation to identify custom ‘barcode’ regions of less than 30 polymorphisms within the span of a single ‘read’, amplification and sequencing of the ‘barcode’, generation of a custom database of polymorphisms, and quantitation of the relative abundance of genotypes. The pipeline and workflow were validated in a ‘wild type’ Alphabaculovirus isolate, Helicoverpa armigera single nucleopolyhedrovirus HaSNPV-AC53 and a tissue-culture derived strain HaSNPV-AC53-T2. The approach was validated by comparison of polymorphisms in amplicons and shotgun data, and by comparison of predicted dominant and co-dominant genotypes with Sanger sequences. The computational power required to generate and search the database effectively limits the number of polymorphisms that can be included in a barcode to 30 or less. The approach can be used in quantitative analysis of the ecology and pathology of non-model organisms. View Full-Text

Keywords: bioinformatics; baculoviruses; metapopulation; meta-barcoding; MetaGaAP; HaSNPV-AC53; community analysis bioinformatics; baculoviruses; metapopulation; meta-barcoding; MetaGaAP; HaSNPV-AC53; community analysis





Author: Christopher Noune and Caroline Hauxwell *

Source: http://mdpi.com/



DOWNLOAD PDF




Related documents